Insulin is expressed by enteroendocrine cells during human fetal development

Codes and single cell data for  "Insulin is expressed by enteroendocrine cells during human fetal development" paper.

Folder: Cell_Ranger_output
Data produced using 10x sequencing.
This folder contains all the Cell Ranger output raw files from all 6 subjects used for single cell RNA sequencing (2x Neonatal- S1056, S1127, 2x fetal 21 weeks GA- S1100A, S1102, 2x fetal 23weeks GA S1130, S1143).
Each subject has two 10X runs- one done on CD45 negatively selected small intestinal cells and the other on non-selected small intestinal cells.

Folder: Matlab_codes_and_struct
Done on Matlab R2019b
This folder contains two scripts and their input files.
1. Global_transcriptome_similarity_Matlab.m - Matlab script to create the distance from adult beta cells from Extended Data Fig 2
2. sturcture_for_global_similarity.mat - input file for "Global_transcriptome_similarity_Matlab.m" script
3. SCENIC_analysis_matlab.m -  Matlab script to create clustergram of transcription factors with the most differential activities in the different cell types from Extended Data Fig 3
4. EECs_mat_file.mat - input file for "SCENIC_analysis_matlab.m" script

Folder: Seurat_pipline_and_background_subtraction
Done with Seurat package version 3.2.2
This folder contains R scripts for Seurat analysis and script for background (BG) subtraction of the data.
1. BG_subtraction_before_seurat.R - Script that creates a BG subtracted matrix for each Cell Ranger output before Seurat analysis.
2. seurat_pipline_all_cells.R - Script for Seurat analysis for the full atlas and the Enteroendocrine subset.

Folder: Count_tables
This folder contains three BG subtracted UMI tables and their additional metadata.
1. BG_subtracted_count_table_all_cells_before_filt.txt - BG subtracted UMI table of all cells before Seurat filtration and analysis (input file for "seurat_pipline_all_cells.R" script).
2. Metadata_all_cells_before_filteration.xlsx - Metadata for "BG_subtracted_count_table_all_cells_before_filt.txt " (input file for "seurat_pipline_all_cells.R" script).
3. BG_subtracted_count_table_all_cells_after_filt.txt - BG subtracted UMI table of all cells after Seurat filtration and analysis.
4. Metadata_all_cells_after_filteration.xlsx - Metadata for "BG_subtracted_count_table_all_cells_after_filt.txt".
5. BG_sub_count_table_enteroendocrine_cells.txt - BG subtracted UMI table of enteroendocrine cells subset after Seurat filtration and analysis.                                                                                                                                                                                              
6. Metadata_enteroendocrine_cells.xlsx - Metadata for "BG_sub_count_table_enteroendocrine_cells.txt".